The government is preparing to cut spending on its flagship academy programme, with schools' sponsors told to expect a reduction in funding for each new academy school as soon as next year.

Academy leaders have been told to brace themselves for tighter spending from 2010 in the first admission that the government is preparing to reduce its spending in some areas of education.

The revelation prompted accusations from the Conservatives that Labour is backing away from the Blairite scheme of independent state schools, but the government said it was still planning to expand the number of academies.

Academies, which have received nearly £5bn in funding since their launch in 2001, have been told by government officials to "tighten their belts" in preparation for the downturn, according to Sir Bruce Liddington, head of a chain of academies and former chief civil servant for the programme. There are 130 academies currently open, with another 67 due to open in the next two weeks and 100 planned for September next year.

Some schools, principally small rural primary schools, may close as spending is reduced from next year, Liddington said.

Edutrust Academies Charitable Trust (EACT), the academy sponsorship charity he is responsible for, is preparing to step in to rescue small rural schools by running them as chains to cut costs and save them from closure.

The move could be part of a major expansion of academy sponsorship into the primary sector, Liddington said. "It's anticipated that there will be cuts in the amount of money that goes towards new academies that are opening … We're all anticipating, and officials are encouraging us to anticipate, that any academies we open from next year will not be as well funded as the academies opening this year," he said.

He said funding was in place to set up the schools opening next month and to build nearly 100 the year after, adding: "But the signs are that we are going to have to tighten our belts." Spending on schools had risen dramatically under Labour, he said. In 1997 the government spent on average £3,030 for every pupil in England, compared with £6,350 this year, but this could not be sustained as government spending was tightened.

"The relative prosperity that schools have enjoyed, that have led to things such as the huge expansion of classroom assistants, the number of programmes that attract funding around Every Child Matters as opposed to just attainment, these sorts of things … they must be vulnerable," he said. "There's a whole load of primary schools in rural areas all over the country, which, if there is a downturn in funding, are going to find they simply cannot afford to stay open and that would be an absolute tragedy." "We stand ready in the EACT to work with local authorities to come up with chains of primary schools, be they academies or not, to make sure that the economies of scale you can have if you have a chain lead to the protection of high quality provision in rural areas rather than closure, which I think is a real threat."

Chains of schools are now central to the government's school improvement plans, included in its last schools white paper. The chains could be run by academy sponsors or sponsors of "trust" schools. Ministers released data this week showing that exam results in academies had risen faster than the national average. Of the 63 academies that received GCSE results this year and last, the proportion of pupils getting five good GCSEs with English and maths increased by 5.1 percentage points to an average of 35%. The national improvement last year was 2.5 percentage points.

Nick Gibb, the shadow schools minister, called on the government to reveal what cuts it plans for frontline services, adding: "It's interesting that the first thing Ed Balls reaches for when it comes to cuts is the academy programme. It's evidence that Ed Balls does not support academies."

Acknowledging that taxpayers wanted to see value for money, the schools minister, Diana Johnson, said "natural savings" made by the government in start-up funding for academies since February 2008 would allow the government to "increase the rate at which we open academies and this year will see the largest number of academies open in one year."